Sleep spindles (SP) are one of the few known electrophysiological neuronal biomarkers of interindividual differences in cognitive abilities and aptitudes. Recent simultaneous electroencephalography with functional magnetic resonance imaging (EEG-fMRI) studies suggest that the magnitude of the activation of brain regions recruited during spontaneous spindle events is specifically related to Reasoning abilities. However, it is not known if the relationship with cognitive abilities differs between uncoupled spindles, uncoupled slow waves (SW), and coupled SW-SP complexes, nor have the functional-neuroanatomical substrates that support this relationship been identified. Here, we investigated the functional significance of activation of brain areas recruited during SW-coupled spindles, uncoupled spindles, and uncoupled slow waves. We hypothesize that brain activations time locked to SW-coupled spindle complexes will be primarily associated to Reasoning abilities, especially in subcortical areas. Our results provide direct evidence that the relationship between Reasoning abilities and sleep spindles depends on spindle coupling status. Specifically, we found that the putamen and thalamus, recruited during coupled SW-SP events were positively correlated with Reasoning abilities. In addition, we found a negative association between Reasoning abilities and hippocampal activation time-locked to uncoupled SWs that might reflect a refractory mechanism in the absence of new, intensive hippocampal-dependent memory processing.